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NM_003383.5(VLDLR):c.464G>C (p.Ser155Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 29, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000130700.3
Variation ID:
130700
Description:
single nucleotide variant
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NM_003383.5(VLDLR):c.464G>C (p.Ser155Thr)

Allele ID
136146
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.2
Genomic location
9: 2643175 (GRCh38) GRCh38 UCSC
9: 2643175 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.2643175G>C
NC_000009.12:g.2643175G>C
NM_003383.5:c.464G>C MANE Select NP_003374.3:p.Ser155Thr missense
... more HGVS
Protein change
S155T, S114T
Other names
-
Canonical SPDI
NC_000009.12:2643174:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00300 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00286
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00277
Exome Aggregation Consortium (ExAC) 0.00082
The Genome Aggregation Database (gnomAD) 0.00296
The Genome Aggregation Database (gnomAD), exomes 0.00073
1000 Genomes Project 0.00300
Links
ClinGen: CA155907
dbSNP: rs34080096
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 19, 2016 RCV000118814.5
Likely benign 1 criteria provided, single submitter Dec 31, 2019 RCV000882448.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
VLDLR - - GRCh38
GRCh37
227 444

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 19, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000515252.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Mar 13, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231049.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001025688.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000153461.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=VLDLR - - - -

Text-mined citations for rs34080096...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 27, 2021